Contacts of the helix formed by residues 304 - 312 (chain B) in PDB entry 6EZG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 304 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296B ILE* 4.2 12.7 - - - +
303B THR* 1.3 79.3 - - - +
305B LEU* 1.3 64.9 + - - +
306B GLU* 3.8 6.1 + - - +
307B SER* 2.7 47.3 + - - -
308B MET* 3.0 8.5 + - - +
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B MET* 5.3 1.8 - - + -
211B LEU* 3.8 20.3 - - + +
229B PRO* 3.2 35.2 - - + +
230B ASN* 3.9 15.0 - - + -
235B SER* 4.1 16.8 - - - +
296B ILE* 3.9 19.1 - - + +
301B PHE* 3.6 36.3 - - + -
303B THR 3.6 1.2 + - - -
304B SER* 1.3 72.6 - - - +
306B GLU* 1.3 58.4 + - - +
308B MET* 3.2 8.0 + - - +
309B LEU* 2.9 35.9 + - + +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ASN* 5.9 0.5 - - - +
304B SER* 3.2 5.9 - - - +
305B LEU* 1.3 79.2 - - - +
307B SER* 1.3 57.7 + - - +
309B LEU* 3.3 10.6 + - - +
310B ASN* 2.9 44.4 + - - +
406B HIS* 2.8 40.7 + - - -
410B LYS* 3.8 13.2 + - - -
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Residues in contact with SER 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B THR* 2.8 29.6 + - - -
304B SER* 2.7 28.4 + - - -
306B GLU* 1.3 76.6 - - - +
308B MET* 1.3 56.0 + - - +
310B ASN* 3.6 9.3 - - - +
311B SER* 3.0 32.8 + - - -
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Residues in contact with MET 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU* 3.2 48.2 - - + +
216B ARG* 4.0 0.7 - - - +
301B PHE* 4.4 9.6 - - - -
302B PRO* 3.7 25.1 - - + -
303B THR* 3.4 27.8 - - - +
304B SER 3.0 19.4 + - - +
305B LEU* 3.6 8.1 - - - +
307B SER* 1.3 76.3 - - - +
309B LEU* 1.3 62.3 + - - +
311B SER* 3.9 5.8 - - - -
312B GLY 3.2 2.3 + - - -
313B ASN* 2.9 63.9 + - - +
314B PHE* 3.5 3.3 - - - -
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU* 4.2 17.3 - - + -
229B PRO* 5.7 1.6 - - + -
230B ASN* 4.7 13.7 - - + -
305B LEU* 2.9 23.0 + - + +
306B GLU* 3.6 17.0 - - - +
308B MET* 1.3 77.0 - - - +
310B ASN* 1.3 64.3 + - - +
312B GLY 3.6 1.4 + - - -
314B PHE* 3.6 27.2 - - + -
406B HIS* 4.5 10.1 - - + -
407B PHE* 3.9 38.1 - - + +
410B LYS* 4.0 37.5 - - + +
411B TYR* 5.2 2.0 - - + +
414B PHE* 4.2 5.9 - - - -
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Residues in contact with ASN 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B GLU* 2.9 39.4 + - - +
307B SER* 3.6 8.7 - - - +
308B MET 3.2 0.2 - - - -
309B LEU* 1.3 80.0 - - - +
311B SER* 1.3 60.1 + - - +
312B GLY 3.5 1.0 + - - -
410B LYS* 2.7 32.3 + - - +
414B PHE* 3.7 12.0 - - - -
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Residues in contact with SER 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B SER 3.0 17.5 + - - -
308B MET* 3.9 0.2 - - - -
310B ASN* 1.3 75.5 - - - +
312B GLY* 1.3 60.6 + - - +
313B ASN* 3.2 23.7 + - - +
316B LYS* 5.3 0.5 + - - -
414B PHE* 4.0 9.9 - - - -
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Residues in contact with GLY 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B MET 3.2 3.4 + - - -
309B LEU 3.6 0.6 + - - -
310B ASN 3.3 4.6 + - - -
311B SER* 1.3 78.8 - - - +
313B ASN* 1.3 58.6 + - - +
314B PHE* 2.9 26.9 + - - +
316B LYS* 2.6 31.4 + - - -
414B PHE* 3.5 25.0 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il